Aleotti had already shown what he could do before the ducal nomination and was appreciated at court as a cartographer. In the aftermath of the devastating earthquake that shook Ferrara and district in 1570 he scored even more points as he worked heroically to recover various important buildings. In those same years he also came up with a plan for the draining of the Gualtieri valleys, a district near Parma that was owned by the Bentivoglio family.
In 1579 Aleotti was called in to restore the Fortezza di Montalfonso in Garfagnana and, in Ferrara, he completed the campanile of the Cathedral. In 1580, Duke Alfonso II ordered him to complete the reclamation of the Polesine area near Ferrara, a work already underway. After having built in Ferrara the Grand Loggia of the Palazzina Marfisa, Aleotti designed and began work on Castle Bentivoglio in Gualtieri. In the following year, he designed Palazzo Bentivoglio in Ferrara.
To this same period also belongs the construction of the Walls of San Giacomo, while in 1597, after having designed the gardens of Campogalliano near Modena, he built the Oratorio della Rotonda in Castel Tedaldo. It ought to be remembered that, in 1598, following Cesare d'Este's handover of power to Pope Clement VIII, Aleotti refused a proposal from Venice to build new defences and a new waterworks.
But Aleotti did accept when the Camera Apostolica and the council of Ferrara confirmed him as public engineer to the city and it was in that capacity that he made a detailed hydrographic study of the area's complex network of rivers and canals and a topographical plan of the Ferrara area, used by cartographers to this day.
In 1600, he designed the chapel of Santa Giustina and the façade of Palazzo Costabili; and, in Argenta, he built the Church of Santa Caterina Martire. In 1602, he was nominated "architect TO the Fortress OF Ferrara". In the following year he designed and built the Torre dell'Arengo (today dell'Orologio) and the Torre del Mercato, as well as the Oratory of Santa Margherita and, in Parma, the Church of Santa Maria del Quartiere. Two years later, he was to build the Teatro dell'Accademia Ferrarese degli Intrepidi. Then he went on to design the Campanile di San Francesco, the Ponte del Canale Panfilio and the Portale di San Paolo, while in Faenza he designed the Square and the Torre dell'Orologio.
In Comacchio he worked on the famous Portico dei Cappuccini and, in 1608, he was master of works for the extensions ordered to the fortress in Ferrara, where he also finished the façade of Palazzo Paradiso. In 1610 he made Ariosto's tomb, the Tower in the Palazzo dell'Università, and the funeral monument dedicated to the marquis Bentivoglio.
Still in 1610, working to plans by Balestri, he was master of works for the Chiesa della Celletta in Ancona where he also designed the Oratorio della Santa Croce, while in Ferrara he designed the Oratorio di Santo Spirito and the Chiesa dei Cappuccini as well as the churches of Santa Barbara and San Carlo. In Ferrara he also designed the theatre made in the "Sala Grande" in Palazzo di Corte. Between 1615 and 1620 he designed and built the renowned Teatro Farnese in Parma, known and admired all over the world.
In the same period, he completed Ferrara's Chiesa della Fortezza and built the campanile of San Benedetto's, the church of Santa Francesca Romana and the central chapel of the church of Sant'Andrea. In 1622 Aleotti built, at Scandiano near Reggio Emilia, the Torresino della Rocca, drew up plans for the regulation of the waters of the river Trebbia, between Parma and Piacenza, and completed the reclamation of the valleys Zelo and Stienta. Giovan Battista Ricotti died in Ferrara in 1636.
His death marks the loss of one of the most interesting men of the Renaissance.